In many species, single nucleotide polymorphism (SNP)-trait associations have been detected through genome-wide association studies (GWASs). In addition to the discovery of trait-associated variants and their biological function, there is increasing interest in making predictions of complex trait phenotypes from genotype data for individuals in plant and animal breeding, experimental organisms and human populations. These predictions are based upon selections of SNPs (or other genomic variants) and estimation of their effects in a discovery sample, followed by validation in an independent sample with known phenotypes, and ultimately application to samples with unknown phenotypes (FIG 1).
